Tree Genetics & Genomes

, 13:37 | Cite as

Transcriptome profiling of Eucalyptus nitens reveals deeper insight into the molecular mechanism of cold acclimation and deacclimation process

  • José Gaete-Loyola
  • Catalina Lagos
  • María F. Beltrán
  • Sofía Valenzuela
  • Verónica Emhart
  • Marta Fernández
Original Article
Part of the following topical collections:
  1. Gene Expression


Eucalyptus nitens (H. Deane & Maiden) is a fast-growing species used principally for pulpwood and solid-wood production. Due to its cold tolerance, it is preferred over other Eucalyptus species at high elevations. To get a deeper insight in the molecular mechanisms of cold acclimation, the transcriptome profiling by RNA-Seq in plants of E. nitens under cold acclimation and deacclimation process was compared in order to identify differentially expressed genes (DEGs). Transcriptomes from control, cold acclimated to chilling temperature, cold acclimated at freezing temperature, and deacclimation condition were compared using Eucalyptus grandis as reference genome. The differential expression analysis allowed the identification of a total of 1600 DEGs out of which 1088 and 1071 were identified in response to cold acclimation and deacclimation, respectively. The gene ontology analysis revealed that DEGs were significantly enriched in response to stimulus, response to abiotic stimulus, membrane, catalytic activity, and cell periphery. Furthermore, the biochemical pathways analysis revealed a large number of DEGs represented in the biosynthesis of phenylpropanoids, specifically flavonoid biosynthesis likely to support ROS scarvening, genes related to photosynthesis, genes that take part in glycolysis/gluconeogenesis related to starch biosynthesis pathway, and genes represented in carotenoid biosynthesis pathway suggesting a role in the regulation of ABA synthesis, which has been previously involved in stress tolerance. A total of 115 DEGs corresponding to transcription factors were identified, being the most represented families AP2, MYB, and WRKY. Expression of six DEGs was validated using qRT-PCR that further supported the in silico results. The present study provides a comprehensive view of global gene expression and revealed valuable information about the dynamic and complex nature of gene expression occurring during cold acclimation and deacclimation process in E. nitens.


RNA-Seq In silico gene expression Differentially expressed genes Transcription factors Cold acclimation-responsive genes qRT-PCR 



Financial support came from Fondecyt Iniciación 11121559 and Genómica Forestal S.A. We would like to thank Conicyt for scholarship to CL and MFB.

Author’s contributions

VE provided plant material. CL and MFB performed growth chamber experiments. JGL performed the RNA-Seq data analysis. CL and MFB performed the validation of reference genes and CA-responsive genes by qRT-PCR. JGL, CL, and MF drafted the manuscript. MF initiated, designed, and led the project. SV contributed to experimental design. All authors contributed to manuscript preparation and editing. All authors read and approved the final manuscript.

Data archiving statement

The short-read sequences data have been submitted to the NCBI Sequence Read Archive ( under accession SRP066573. The Bioproject ID related to this paper is PRJNA303180.

Supplementary material

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© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  1. 1.Centro de BiotecnologíaUniversidad de ConcepciónConcepciónChile
  2. 2.Facultad de Ciencias ForestalesUniversidad de ConcepciónConcepciónChile
  3. 3.Facultad de Ciencias BiológicasUniversidad de ConcepciónConcepciónChile
  4. 4.Forestal Mininco S.A.Los AngelesChile

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